[gmx-developers] GROMACS 2018.8 PERFORMANCE
Navneet Kumar
navneetcdl at gmail.com
Fri Dec 11 20:02:54 CET 2020
Hello Everyone!
I have installed Gromacs 2018.8 on two different workstations. Workstation
having NVIDIA Quadro RTX 5000 (3072 CUDA Cores) gives better performance
(approx 350 ns per day for lysozyme) than the NVIDIA Quadro RTX 6000 (4608
CUDA Cores) (approx 200 ns per day). Please see the log file for the both.
It seems there are some problems while installation. Please help.
______________________________________________________________________________________________________________________________________
NVIDIA Quadro RTX 6000,
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2018.8
Executable: /usr/local/gromacs-2018.8/bin/gmx
Data prefix: /usr/local/gromacs-2018.8
Working dir: /home/pglab-6000/Desktop/new
Command line:
gmx mdrun -v -deffnm md_0_1
GROMACS version: 2018.8
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: CUDA
SIMD instructions: AVX_512
FFT library: fftw-3.3.8-sse2-avx
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
Built on: 2020-12-11 17:22:07
Built by: root at pglab6000-ThinkStation-P520 [CMAKE]
Build OS/arch: Linux 5.4.0-54-generic x86_64
Build CPU vendor: Unknown
Build CPU brand: Unknown
Build CPU family: 0 Model: 0 Stepping: 0
Build CPU features: Unknown
C compiler: /usr/bin/gcc-7 GNU 7.5.0
C compiler flags: -mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler: /usr/bin/g++-7 GNU 7.5.0
C++ compiler flags: -mavx512f -mfma -std=c++11 -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
CUDA compiler: /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on
Sun_Jul_28_19:07:16_PDT_2019;Cuda compilation tools, release 10.1, V10.1.243
CUDA compiler
flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;;
;-mavx512f;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
CUDA driver: 10.20
CUDA runtime: 10.10
Running on 1 node with total 10 cores, 20 logical cores, 1 compatible GPU
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) W-2155 CPU @ 3.30GHz
Family: 6 Model: 85 Stepping: 4
Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh
cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq
pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt
x2apic
Number of AVX-512 FMA units: 2
Hardware topology: Basic
Sockets, cores, and logical processors:
Socket 0: [ 0 10] [ 1 11] [ 2 12] [ 3 13] [ 4 14] [
5 15] [ 6 16] [ 7 17] [ 8 18] [ 9 19]
GPU info:
Number of GPUs detected: 1
#0: NVIDIA Quadro RTX 6000, compute cap.: 7.5, ECC: no, stat:
compatible
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------
--------------------------------------------------------------------------------------------------------------------
NVIDIA Quadro RTX 5000
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx mdrun, version 2018.8
Executable: /usr/local/gromacs-2018.8/bin/gmx
Data prefix: /usr/local/gromacs-2018.8
Working dir: /home/pglab-5000/Desktop/Test_Simualtion
Command line:
gmx mdrun -v -deffnm md_0_1
GROMACS version: 2018.8
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support: CUDA
SIMD instructions: AVX_512
FFT library: fftw-3.3.8-sse2-avx
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
Built on: 2020-12-09 23:44:03
Built by: root at pglab5000-ThinkStation-P520 [CMAKE]
Build OS/arch: Linux 5.4.0-42-generic x86_64
Build CPU vendor: Unknown
Build CPU brand: Unknown
Build CPU family: 0 Model: 0 Stepping: 0
Build CPU features: Unknown
C compiler: /usr/bin/gcc-8 GNU 8.4.0
C compiler flags: -mavx512f -mfma -O3 -DNDEBUG -funroll-all-loops
-fexcess-precision=fast
C++ compiler: /usr/bin/c++ GNU 9.3.0
C++ compiler flags: -mavx512f -mfma -std=c++11 -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
CUDA compiler: /usr/bin/nvcc nvcc: NVIDIA (R) Cuda compiler
driver;Copyright (c) 2005-2019 NVIDIA Corporation;Built on
Sun_Jul_28_19:07:16_PDT_2019;Cuda compilation tools, release 10.1, V10.1.243
CUDA compiler
flags:-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_70,code=sm_70;-gencode;arch=compute_75,code=compute_75;-use_fast_math;-D_FORCE_INLINES;;
;-mavx512f;-mfma;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;
CUDA driver: 11.10
CUDA runtime: 10.10
Running on 1 node with total 10 cores, 20 logical cores, 1 compatible GPU
Hardware detected:
CPU info:
Vendor: Intel
Brand: Intel(R) Xeon(R) W-2155 CPU @ 3.30GHz
Family: 6 Model: 85 Stepping: 4
Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl clfsh
cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop_tsc pcid pclmuldq
pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt
x2apic
Number of AVX-512 FMA units: 2
Hardware topology: Basic
Sockets, cores, and logical processors:
Socket 0: [ 0 10] [ 1 11] [ 2 12] [ 3 13] [ 4 14] [
5 15] [ 6 16] [ 7 17] [ 8 18] [ 9 19]
GPU info:
Number of GPUs detected: 1
#0: NVIDIA Quadro RTX 5000, compute cap.: 7.5, ECC: no, stat:
compatible
_____________________________________________________________________________________________________________________________________________________
--
Thanks & Regards
_______________________________________________________
[image: photo]
*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647 <+918017967647> |
E navneetcdl at gmail.com <navneetcdl at gmail.com>
<http://www.linkedin.com/in/navneet-kumar-74391814a/>
<http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
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